How do I install gget for use with Claude Code?

You can install gget in your environment using 'uv pip install gget' or 'pip install gget'. Some specialized modules like AlphaFold may require additional setup steps.

What databases can gget access?

gget provides unified access to over 20 biological databases including Ensembl, UniProt, NCBI, AlphaFold, ARCHS4, Enrichr, OpenTargets, and COSMIC.

Is the data provided by gget up to date?

The gget developers test the modules biweekly and release updates whenever underlying database structures change to ensure reliable data retrieval.

Can I use gget for protein structure prediction?

Yes, gget includes a dedicated AlphaFold module that allows for simplified 3D protein structure and multimer prediction directly from amino acid sequences.

Does gget support both CLI and Python usage?

Yes, all gget modules are designed to work interchangeably as command-line tools and as native Python functions, making it flexible for different workflows.

gget Bioinformatics Tool

Name: gget Bioinformatics Tool
Author: Activer007

byActiver007

Data Science & ML

Streamlines bioinformatics workflows by providing a unified CLI and Python interface to over 20 genomic and proteomic databases.

About

gget is an essential toolkit for bioinformaticians and researchers, offering streamlined access to a vast array of biological data through a consistent interface. It enables users to perform rapid BLAST/BLAT searches, download reference genomes, retrieve gene metadata, and even predict protein structures with AlphaFold without needing to navigate multiple complex web portals. By consolidating diverse database APIs into a single tool, gget significantly reduces the friction of data gathering and preprocessing for genomic analysis, making it an ideal companion for scientific research and computational biology within Claude Code.

Key Features

Unified access to 20+ databases including Ensembl, UniProt, and NCBI
Functional enrichment and disease association analysis through Enrichr and OpenTargets
Rapid sequence alignment using BLAST, BLAT, and DIAMOND
0 GitHub stars
Simplified 3D protein structure prediction via AlphaFold2 integration
Gene expression and correlation queries via ARCHS4 and CELLxGENE

Use Cases

Automating reference genome downloads and gene metadata retrieval for large-scale analysis pipelines
Running sequence alignments and structural predictions directly from the command line or Python scripts
Investigating gene-disease associations and expression patterns across specific tissues and cell types

About

Key Features

Unified access to 20+ databases including Ensembl, UniProt, and NCBI
Functional enrichment and disease association analysis through Enrichr and OpenTargets
Rapid sequence alignment using BLAST, BLAT, and DIAMOND
0 GitHub stars
Simplified 3D protein structure prediction via AlphaFold2 integration
Gene expression and correlation queries via ARCHS4 and CELLxGENE

Use Cases

Automating reference genome downloads and gene metadata retrieval for large-scale analysis pipelines
Running sequence alignments and structural predictions directly from the command line or Python scripts
Investigating gene-disease associations and expression patterns across specific tissues and cell types